TkA07G009740 | RubberDandelionOmics

Gene overview

TkA07G009740

Reference: TK1151 Chr: Chr07 Coordinates: 2639440-2647380 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2954 bp · TkA07G009740|TK1151|cDNA

TATAGAAACAGAAGTACAAGGGTTAAATGCGCATAGCTTAATAGTTTAGGGCAAATTTTTGAAACTTAACCAAGCACCGTCATTATAGGATTCTTGACTTAAGTGAACGGATGCAAGAAATAGTCAAAATCCTCTAAAAACTCCCCAACTTAACGATCACCGTTACCGGCCACCGGACGTCACCGTATTCCGCCGTCATCCTACAGTCATCATCGTCATTCACCGGAGATCAGAATATTTCGAGTGATTAGTTATAGATA...

CDS

Download CDS FASTA

1416 bp · TkA07G009740|TK1151|CDS

ATGGCATTGCAACGTACAATAGAATTTGAGGAAGAATTGGCAGAGAAGTTTGGTGGTAGTGGTAGTGGTAGTAGCAGAAATGTGACAAATGATTTTGAGGAAACAAATAAATCAGAAAGTAATAATAATAATCAAATTGTACAAGACATTCGTAAGAAATATGAGAAAAAACTTGCTGCACATCAGGATGATGATAAAGATTTAGCTGTGCCTGGAGCAGGGTTCAATTTTCGTGGAATCATATCATCTTGCTTTGAACC...

Protein

Download Protein FASTA

471 aa · TkA07G009740|TK1151|PROTEIN

MALQRTIEFEEELAEKFGGSGSGSSRNVTNDFEETNKSESNNNNQIVQDIRKKYEKKLAAHQDDDKDLAVPGAGFNFRGIISSCFEPHLMVYVDFEEKTLMDNLEKLVQEETWDMDDGQTNILSSSMQVFLIIRRSLKRCSALTKNQTLLNLFKVFKRVLKAYATKLFMKLPKGGTGIVAAATGMDGQIKTSDKDERMICYIVNTAEYCHKTAGELAENVSKIIDTQLADAVDMSEVEDEFSAVITKALVTLVNGLETKF...

Flanking Sequence Download

Sequence orientation and download details

Upstream/downstream are capped at 10000 bp per side. Negative-strand genes are reverse-complemented so the final FASTA follows transcriptional 5′→3′ orientation.

ID Mapping

Input ID	`TkA07G009740`
TK1151 ID	TkA07G009740
OH-1004 ID	LXL04_026818
Relationship / confidence	Sequence Supported Annotation Or Model Conflict / Review
Protein identity (%)	96.900
Protein coverage (%)	TK1151 95.117 / OH-1004 54.324 Coverage and evidence Coverage is the aligned span of the best-scoring HSP divided by representative protein length. A homolog match does not establish functional validation.
Source version	TK1151 / GWHBCHF00000000

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SNP / Indel variants and carrier samplesCRA009020 · TK1151

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID TkA07G009740

Location Chr07:2639440-2647380 (+)

Description Similar to VPS53: Vacuolar protein sorting-associated protein 53 A

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g50500`	Acts as a component of the GARP complex that is involved in retrograde transport from early and late endosomes to the trans-Golgi network (TGN).	Mutation in a homolog of yeast Vps53p accounts for the heat and osmotic hypersensitive phenotypes in Arabidopsis hit1-1 mutant.2006 · DOI: 10.1007/s00425-005-0216-6 The POK/AtVPS52 protein localizes to several distinct post-Golgi compartments in sporophytic and gametophytic cells.2008 · DOI: 10.1093/jxb/ern162 Involvement of the Arabidopsis HIT1/AtVPS53 tethering protein homologue in the acclimation of the plasma membrane to heat stress.2011 · DOI: 10.1093/jxb/err060 The Arabidopsis hit1-1 mutant has a plasma membrane profile distinct from that of wild-type plants at optimal growing temperature.2011 · DOI: 10.4161/psb.6.8.15842

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_026818 · GCA_047496595.1_OSU_TarKok_2.0. These OH1004 annotations are retrieved through ID mapping; the Arabidopsis/rice table below uses protein alignments from the query reference.

GO annotations (OH1004 source)

GO:0006622 protein targeting to lysosome Biological Process

GO:0006890 retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum Biological Process

GO:0006970 response to osmotic stress Biological Process

GO:0007009 plasma membrane organization Biological Process

GO:0007041 lysosomal transport Biological Process

GO:0009408 response to heat Biological Process

GO:0010286 heat acclimation Biological Process

GO:0015031 protein transport Biological Process

GO:0032456 endocytic recycling Biological Process

GO:0042147 retrograde transport, endosome to Golgi Biological Process

GO:0090119 vesicle-mediated cholesterol transport Biological Process

GO:0000139 Golgi membrane Cellular Component

KEGG gene cross-reference

ath:AT1G50500

ath:AT1G50970

mmu:68299

pon:100173757

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

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Gene expression

View expression in different studies, tissues and treatments. Results are presented separately by study and measurement unit.

View expression for this gene

Data sources and gene correspondence

Expression data come from public transcriptome studies. Reference genomes, sample metadata and measurement units are shown with the results. Ambiguous cross-reference correspondences do not select an expression record automatically; missing values do not mean zero expression.

Subcellular Localization Top 5

Computational predictions or homology annotations below do not replace localization experiments.

Cytoplasm0.540

Rank 1 · TkA07G009740 · TK1151

Golgi apparatus0.466

Rank 2 · TkA07G009740 · TK1151

Cell membrane0.145

Rank 3 · TkA07G009740 · TK1151

Lysosome / Vacuole0.126

Rank 4 · TkA07G009740 · TK1151

Endoplasmic reticulum0.118

Rank 5 · TkA07G009740 · TK1151

LocPro · Direct prediction · Computational prediction, not experimental localization

Open Subcellular Module

Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF04100Vps53_N1-111 aa

PF29355IOC2_N7-59 aa

PF12081GldM_1st28-60 aa

PF16854VPS53_C34-55 aa

PF17027Bromo_TP_like40-160 aa

PF17944Arg_decarbox_C48-60 aa

PF04437RINT1_TIP179-357 aa

PF06292MUN82-269 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA07G009740	`PF04100`	Vps53_N	1	111	2.9e-14	53.6
TkA07G009740	`PF29355`	IOC2_N	7	59	0.88	10.6
TkA07G009740	`PF12081`	GldM_1st	28	60	0.86	10.2
TkA07G009740	`PF16854`	VPS53_C	34	55	3.2e-15	57.2
TkA07G009740	`PF17027`	Bromo_TP_like	40	160	0.14	12.9
TkA07G009740	`PF17944`	Arg_decarbox_C	48	60	0.13	13.5
TkA07G009740	`PF04437`	RINT1_TIP1	79	357	2e-05	24.4
TkA07G009740	`PF06292`	MUN	82	269	0.014	15.1
TkA07G009740	`PF10191`	COG7	83	166	3.1e-05	23.2
TkA07G009740	`PF17944`	Arg_decarbox_C	90	117	0.13	13.5
TkA07G009740	`PF29355`	IOC2_N	92	162	0.88	10.6
TkA07G009740	`PF12081`	GldM_1st	160	234	0.86	10.2
TkA07G009740	`PF17944`	Arg_decarbox_C	208	227	0.13	13.5
TkA07G009740	`PF16320`	Ribosomal_L12_N	250	267	1.4	9.4
TkA07G009740	`PF16854`	VPS53_C	340	418	3.2e-15	57.2
TkA07G009740	`PF17944`	Arg_decarbox_C	409	431	0.13	13.5

Arabidopsis / Rice Protein Homology

Only Arabidopsis and rice are shown. Swiss-Prot entries are reviewed; TrEMBL entries are supplementary sequence candidates. Similarity is not experimental validation.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q0WQF4`	Arabidopsis thaliana	sp\|Q0WQF4\|VP53A_ARATH Vacuolar protein sorting-associated protein 53 A	72.100%	Swiss-Prot	High

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